BACKGROUND The aim was to investigate the associations between cardiovascular fitness and physical activity, and their relationship to selected coronary heart disease (CHD) risk factors. METHODS This was a cross-sectional study for one week. All participants were Japanese living in the City of Toyota, Japan. Two hundred and twenty-two healthy Japanese (104 men and 118 women), with ages between 20 and 62 years old. Cardiovascular fitness (VO2max) was measured by a progressive submaximal bicycle ergometry test. Physical activity was estimated by an accelerometers attached to the subject's waist for one week, CHD risk factors included blood pressure, fasting levels of blood lipids, and apolipoprotein concentrations. RESULTS Cardiovascular fitness and physical activity were positively related (r = 0.41 in men and 0.65 in women). For both genders, Pearson coefficients as well as age-adjusted partial correlations indicated that fitness was more closely linked to CHD risk factors than activity was. Also, CHD risk factors were analyzed by three groups of fitness and activity levels in both genders, which indicates that subjects who are physically fitter and/or more active tend to have better CHD risk profiles. CONCLUSIONS As favorable CHD risk profile was related to cardiovascular fitness, but not to physical activity in both genders, it can be concluded that fitness may be a more important independent predictor for CHD risk factors than activity measured by accelerometer over one week.